Starting phenix.real_space_refine on Thu Jul 2 10:05:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oqz_13035/07_2026/7oqz_13035.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oqz_13035/07_2026/7oqz_13035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oqz_13035/07_2026/7oqz_13035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oqz_13035/07_2026/7oqz_13035.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oqz_13035/07_2026/7oqz_13035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oqz_13035/07_2026/7oqz_13035.cif" model { file = "/net/cci-nas-00/data/ceres_data/7oqz_13035/07_2026/7oqz_13035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oqz_13035/07_2026/7oqz_13035.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 52 5.16 5 C 5468 2.51 5 N 1196 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-1': 2, 'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-1': 2, 'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-1': 2, 'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-1': 2, 'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.46, per 1000 atoms: 0.18 Number of scatterers: 7996 At special positions: 0 Unit cell: (92.65, 92.65, 76.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 8 15.00 O 1272 8.00 N 1196 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 274.9 milliseconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 84.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 3 through 34 Proline residue: A 10 - end of helix Processing helix chain 'A' and resid 42 through 69 removed outlier: 4.237A pdb=" N PHE A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 115 removed outlier: 4.063A pdb=" N HIS A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 141 removed outlier: 4.424A pdb=" N LYS A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 173 Processing helix chain 'A' and resid 176 through 202 Processing helix chain 'A' and resid 214 through 251 Processing helix chain 'B' and resid 4 through 34 Proline residue: B 10 - end of helix Processing helix chain 'B' and resid 42 through 69 removed outlier: 4.237A pdb=" N PHE B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 115 removed outlier: 4.063A pdb=" N HIS B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 141 removed outlier: 4.424A pdb=" N LYS B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 173 Processing helix chain 'B' and resid 176 through 202 Processing helix chain 'B' and resid 214 through 251 Processing helix chain 'C' and resid 4 through 34 Proline residue: C 10 - end of helix Processing helix chain 'C' and resid 42 through 69 removed outlier: 4.237A pdb=" N PHE C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 115 removed outlier: 4.063A pdb=" N HIS C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 141 removed outlier: 4.423A pdb=" N LYS C 124 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 173 Processing helix chain 'C' and resid 176 through 202 Processing helix chain 'C' and resid 214 through 251 Processing helix chain 'D' and resid 4 through 34 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 42 through 69 removed outlier: 4.237A pdb=" N PHE D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 115 removed outlier: 4.063A pdb=" N HIS D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 141 removed outlier: 4.424A pdb=" N LYS D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 173 Processing helix chain 'D' and resid 176 through 202 Processing helix chain 'D' and resid 214 through 251 657 hydrogen bonds defined for protein. 1971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1104 1.31 - 1.43: 2440 1.43 - 1.56: 4461 1.56 - 1.68: 130 1.68 - 1.81: 81 Bond restraints: 8216 Sorted by residual: bond pdb=" C31 PC1 C 302 " pdb=" O31 PC1 C 302 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C31 PC1 A 301 " pdb=" O31 PC1 A 301 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C31 PC1 B 302 " pdb=" O31 PC1 B 302 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C31 PC1 C 303 " pdb=" O31 PC1 C 303 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C31 PC1 D 303 " pdb=" O31 PC1 D 303 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.94e+01 ... (remaining 8211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 10704 2.87 - 5.73: 324 5.73 - 8.60: 12 8.60 - 11.46: 20 11.46 - 14.33: 8 Bond angle restraints: 11068 Sorted by residual: angle pdb=" O12 PC1 D 303 " pdb=" P PC1 D 303 " pdb=" O14 PC1 D 303 " ideal model delta sigma weight residual 123.67 109.34 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 C 302 " pdb=" P PC1 C 302 " pdb=" O14 PC1 C 302 " ideal model delta sigma weight residual 123.67 109.35 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 302 " pdb=" P PC1 A 302 " pdb=" O14 PC1 A 302 " ideal model delta sigma weight residual 123.67 109.35 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 B 302 " pdb=" P PC1 B 302 " pdb=" O14 PC1 B 302 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 301 " pdb=" P PC1 A 301 " pdb=" O14 PC1 A 301 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 ... (remaining 11063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 4157 14.33 - 28.65: 315 28.65 - 42.98: 80 42.98 - 57.31: 64 57.31 - 71.63: 16 Dihedral angle restraints: 4632 sinusoidal: 1924 harmonic: 2708 Sorted by residual: dihedral pdb=" N PHE A 194 " pdb=" CA PHE A 194 " pdb=" CB PHE A 194 " pdb=" CG PHE A 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.53 58.53 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE B 194 " pdb=" CA PHE B 194 " pdb=" CB PHE B 194 " pdb=" CG PHE B 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.52 58.52 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE D 194 " pdb=" CA PHE D 194 " pdb=" CB PHE D 194 " pdb=" CG PHE D 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.51 58.51 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 811 0.024 - 0.049: 253 0.049 - 0.073: 128 0.073 - 0.098: 20 0.098 - 0.122: 8 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1217 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 130 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ALA A 130 " 0.021 2.00e-02 2.50e+03 pdb=" O ALA A 130 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 130 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ALA B 130 " 0.021 2.00e-02 2.50e+03 pdb=" O ALA B 130 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU B 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 130 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C ALA D 130 " -0.021 2.00e-02 2.50e+03 pdb=" O ALA D 130 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU D 131 " 0.007 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1712 2.79 - 3.31: 8076 3.31 - 3.84: 12946 3.84 - 4.37: 13510 4.37 - 4.90: 25055 Nonbonded interactions: 61299 Sorted by model distance: nonbonded pdb=" O LEU D 125 " pdb=" OG SER D 128 " model vdw 2.257 3.040 nonbonded pdb=" O LEU B 125 " pdb=" OG SER B 128 " model vdw 2.257 3.040 nonbonded pdb=" O LEU C 125 " pdb=" OG SER C 128 " model vdw 2.257 3.040 nonbonded pdb=" O LEU A 125 " pdb=" OG SER A 128 " model vdw 2.257 3.040 nonbonded pdb=" NE1 TRP B 21 " pdb=" OE2 GLU B 53 " model vdw 2.342 3.120 ... (remaining 61294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'B' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'C' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'D' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.800 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 8216 Z= 0.448 Angle : 0.981 14.327 11068 Z= 0.384 Chirality : 0.030 0.122 1220 Planarity : 0.003 0.019 1288 Dihedral : 13.713 71.632 2888 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.51 % Allowed : 3.06 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.83 (0.27), residues: 932 helix: 3.85 (0.17), residues: 780 sheet: None (None), residues: 0 loop : -0.84 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 174 TYR 0.005 0.001 TYR A 229 PHE 0.007 0.001 PHE A 96 TRP 0.008 0.001 TRP D 193 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.45 ( 8216) covalent geometry : angle 0.98066 / 0.38 (11068) hydrogen bonds : bond 0.05845 / 4.20 ( 657) hydrogen bonds : angle 3.97629 / 2.94 ( 1971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 377 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8707 (m-10) cc_final: 0.8269 (m-80) REVERT: A 146 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7623 (mp0) REVERT: A 147 MET cc_start: 0.8447 (ptp) cc_final: 0.8195 (ptt) REVERT: A 211 ASP cc_start: 0.8161 (t0) cc_final: 0.7945 (t0) REVERT: A 215 HIS cc_start: 0.8117 (m-70) cc_final: 0.7588 (m90) REVERT: A 217 ASN cc_start: 0.9221 (m-40) cc_final: 0.8955 (m110) REVERT: B 13 PHE cc_start: 0.8648 (m-10) cc_final: 0.8179 (m-80) REVERT: B 146 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7652 (mp0) REVERT: B 211 ASP cc_start: 0.8173 (t0) cc_final: 0.7937 (t0) REVERT: B 217 ASN cc_start: 0.9219 (m-40) cc_final: 0.8888 (m-40) REVERT: B 227 TRP cc_start: 0.8554 (m100) cc_final: 0.8313 (m100) REVERT: B 235 ILE cc_start: 0.9282 (mt) cc_final: 0.9052 (mt) REVERT: C 13 PHE cc_start: 0.8630 (m-10) cc_final: 0.8138 (m-80) REVERT: C 143 HIS cc_start: 0.7095 (t70) cc_final: 0.6689 (t-90) REVERT: C 146 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7613 (mp0) REVERT: C 211 ASP cc_start: 0.8080 (t0) cc_final: 0.7872 (t0) REVERT: C 217 ASN cc_start: 0.9158 (m-40) cc_final: 0.8836 (m-40) REVERT: C 227 TRP cc_start: 0.8446 (m100) cc_final: 0.8241 (m-10) REVERT: C 235 ILE cc_start: 0.9292 (mt) cc_final: 0.9010 (mt) REVERT: C 242 PHE cc_start: 0.8377 (t80) cc_final: 0.7865 (m-80) REVERT: D 13 PHE cc_start: 0.8523 (m-10) cc_final: 0.8010 (m-80) REVERT: D 146 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7523 (mp0) REVERT: D 149 ASP cc_start: 0.7346 (t70) cc_final: 0.7142 (t0) REVERT: D 217 ASN cc_start: 0.9131 (m-40) cc_final: 0.8868 (m-40) REVERT: D 229 TYR cc_start: 0.9124 (t80) cc_final: 0.8709 (t80) REVERT: D 235 ILE cc_start: 0.9312 (mt) cc_final: 0.9037 (mt) REVERT: D 238 MET cc_start: 0.8067 (mtp) cc_final: 0.7832 (mtp) REVERT: D 242 PHE cc_start: 0.8396 (t80) cc_final: 0.7896 (m-80) outliers start: 4 outliers final: 4 residues processed: 381 average time/residue: 0.0700 time to fit residues: 36.4394 Evaluate side-chains 224 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 220 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain D residue 194 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.0470 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN B 3 ASN B 215 HIS C 34 GLN C 94 HIS D 34 GLN D 215 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.089477 restraints weight = 16583.571| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.66 r_work: 0.3131 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8216 Z= 0.120 Angle : 0.531 11.943 11068 Z= 0.265 Chirality : 0.034 0.123 1220 Planarity : 0.003 0.025 1288 Dihedral : 14.474 75.523 1316 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 14.92 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.81 (0.26), residues: 932 helix: 3.81 (0.16), residues: 780 sheet: None (None), residues: 0 loop : -0.76 (0.54), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 174 TYR 0.004 0.000 TYR D 229 PHE 0.022 0.001 PHE B 4 TRP 0.008 0.001 TRP A 193 HIS 0.006 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 8216) covalent geometry : angle 0.53138 / 0.27 (11068) hydrogen bonds : bond 0.04337 / 3.05 ( 657) hydrogen bonds : angle 3.11304 / 2.37 ( 1971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8581 (mm-30) REVERT: A 124 LYS cc_start: 0.8279 (mmmt) cc_final: 0.8063 (mmmt) REVERT: A 147 MET cc_start: 0.8814 (ptp) cc_final: 0.8443 (ptt) REVERT: A 170 GLU cc_start: 0.9237 (tt0) cc_final: 0.8947 (tt0) REVERT: A 175 ASN cc_start: 0.8850 (m-40) cc_final: 0.8607 (p0) REVERT: A 211 ASP cc_start: 0.7941 (t0) cc_final: 0.7396 (t0) REVERT: A 217 ASN cc_start: 0.9303 (m-40) cc_final: 0.8979 (m-40) REVERT: A 227 TRP cc_start: 0.8837 (m100) cc_final: 0.8594 (m100) REVERT: B 4 PHE cc_start: 0.8655 (t80) cc_final: 0.8450 (t80) REVERT: B 50 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8605 (mm-30) REVERT: B 124 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7965 (mmmt) REVERT: B 146 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7233 (mp0) REVERT: B 170 GLU cc_start: 0.9144 (tt0) cc_final: 0.8896 (tt0) REVERT: B 211 ASP cc_start: 0.8076 (t0) cc_final: 0.7452 (t0) REVERT: B 227 TRP cc_start: 0.8756 (m100) cc_final: 0.8506 (m100) REVERT: C 4 PHE cc_start: 0.8616 (t80) cc_final: 0.8415 (t80) REVERT: C 5 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8253 (ttm170) REVERT: C 53 GLU cc_start: 0.8950 (pt0) cc_final: 0.8505 (pt0) REVERT: C 124 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8075 (mmmt) REVERT: C 129 ASN cc_start: 0.9120 (t0) cc_final: 0.8916 (t0) REVERT: C 170 GLU cc_start: 0.9187 (tt0) cc_final: 0.8931 (tt0) REVERT: C 214 ASP cc_start: 0.6909 (t0) cc_final: 0.6257 (t0) REVERT: C 217 ASN cc_start: 0.9294 (m-40) cc_final: 0.8968 (m-40) REVERT: C 227 TRP cc_start: 0.8665 (m100) cc_final: 0.8410 (m-10) REVERT: C 235 ILE cc_start: 0.9138 (mt) cc_final: 0.8909 (mt) REVERT: D 124 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8180 (mmmt) REVERT: D 149 ASP cc_start: 0.7777 (t70) cc_final: 0.7538 (t0) REVERT: D 170 GLU cc_start: 0.9235 (tt0) cc_final: 0.9018 (tt0) REVERT: D 214 ASP cc_start: 0.6630 (t0) cc_final: 0.6306 (t0) REVERT: D 234 VAL cc_start: 0.9260 (t) cc_final: 0.9055 (p) REVERT: D 242 PHE cc_start: 0.8424 (t80) cc_final: 0.7803 (m-80) outliers start: 24 outliers final: 14 residues processed: 241 average time/residue: 0.0759 time to fit residues: 24.3632 Evaluate side-chains 218 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 215 HIS D 34 GLN D 143 HIS ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.113138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.082253 restraints weight = 16451.991| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.46 r_work: 0.3029 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8216 Z= 0.176 Angle : 0.545 7.152 11068 Z= 0.287 Chirality : 0.036 0.130 1220 Planarity : 0.003 0.032 1288 Dihedral : 13.857 79.035 1316 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.72 % Allowed : 15.69 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.56 (0.26), residues: 932 helix: 3.70 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.79 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 174 TYR 0.006 0.001 TYR A 29 PHE 0.022 0.001 PHE A 242 TRP 0.011 0.001 TRP C 193 HIS 0.005 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 8216) covalent geometry : angle 0.54527 / 0.29 (11068) hydrogen bonds : bond 0.06027 / 4.21 ( 657) hydrogen bonds : angle 3.56547 / 2.70 ( 1971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8995 (mmm-85) cc_final: 0.8546 (mtm110) REVERT: A 49 LEU cc_start: 0.9490 (mt) cc_final: 0.9245 (mt) REVERT: A 50 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8721 (mm-30) REVERT: A 124 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8531 (mmmt) REVERT: A 146 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8113 (mp0) REVERT: A 147 MET cc_start: 0.8710 (ptp) cc_final: 0.8365 (ptt) REVERT: A 170 GLU cc_start: 0.9291 (tt0) cc_final: 0.9026 (tt0) REVERT: A 174 ARG cc_start: 0.9103 (mmm-85) cc_final: 0.8801 (mmt90) REVERT: A 214 ASP cc_start: 0.7196 (t0) cc_final: 0.6509 (t0) REVERT: A 217 ASN cc_start: 0.9375 (m-40) cc_final: 0.9006 (m-40) REVERT: A 229 TYR cc_start: 0.9369 (t80) cc_final: 0.9075 (t80) REVERT: B 49 LEU cc_start: 0.9447 (mt) cc_final: 0.9200 (mt) REVERT: B 50 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8746 (mm-30) REVERT: B 111 LEU cc_start: 0.8913 (mt) cc_final: 0.8668 (mp) REVERT: B 124 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8476 (mmmt) REVERT: B 216 GLU cc_start: 0.8486 (mp0) cc_final: 0.8220 (pm20) REVERT: B 227 TRP cc_start: 0.8863 (m100) cc_final: 0.8533 (m-10) REVERT: C 5 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8368 (ttm170) REVERT: C 50 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8720 (mm-30) REVERT: C 111 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8724 (mp) REVERT: C 124 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8255 (mmmt) REVERT: C 146 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7388 (mp0) REVERT: C 170 GLU cc_start: 0.9309 (tt0) cc_final: 0.9062 (tt0) REVERT: C 214 ASP cc_start: 0.7116 (t0) cc_final: 0.6620 (t0) REVERT: C 227 TRP cc_start: 0.8859 (m100) cc_final: 0.8508 (m-10) REVERT: C 235 ILE cc_start: 0.9179 (mt) cc_final: 0.8954 (mt) REVERT: D 49 LEU cc_start: 0.9552 (mt) cc_final: 0.9256 (mt) REVERT: D 50 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8560 (mm-30) REVERT: D 111 LEU cc_start: 0.8983 (mt) cc_final: 0.8755 (mp) REVERT: D 124 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8356 (mmmt) REVERT: D 129 ASN cc_start: 0.9307 (t0) cc_final: 0.9072 (t0) REVERT: D 146 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7956 (mp0) REVERT: D 149 ASP cc_start: 0.8248 (t70) cc_final: 0.7975 (t0) REVERT: D 170 GLU cc_start: 0.9310 (tt0) cc_final: 0.9044 (tt0) REVERT: D 214 ASP cc_start: 0.6970 (t0) cc_final: 0.6452 (t0) REVERT: D 229 TYR cc_start: 0.9311 (t80) cc_final: 0.9111 (t80) REVERT: D 242 PHE cc_start: 0.8420 (t80) cc_final: 0.7746 (m-80) outliers start: 37 outliers final: 24 residues processed: 237 average time/residue: 0.0754 time to fit residues: 24.0732 Evaluate side-chains 226 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS B 34 GLN B 215 HIS D 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.117365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086721 restraints weight = 16928.155| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.58 r_work: 0.3080 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8216 Z= 0.126 Angle : 0.514 7.435 11068 Z= 0.265 Chirality : 0.035 0.132 1220 Planarity : 0.003 0.030 1288 Dihedral : 13.037 78.053 1316 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.72 % Allowed : 17.73 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.59 (0.27), residues: 932 helix: 3.73 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.83 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 174 TYR 0.004 0.000 TYR D 229 PHE 0.019 0.001 PHE A 13 TRP 0.009 0.001 TRP B 193 HIS 0.005 0.001 HIS D 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 8216) covalent geometry : angle 0.51402 / 0.26 (11068) hydrogen bonds : bond 0.04798 / 3.37 ( 657) hydrogen bonds : angle 3.24222 / 2.47 ( 1971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.9030 (mmm-85) cc_final: 0.8560 (mtm110) REVERT: A 49 LEU cc_start: 0.9471 (mt) cc_final: 0.9224 (mt) REVERT: A 50 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8732 (mm-30) REVERT: A 146 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7436 (mp0) REVERT: A 147 MET cc_start: 0.8743 (ptp) cc_final: 0.8169 (ptt) REVERT: A 213 MET cc_start: 0.6463 (mmm) cc_final: 0.6202 (mmm) REVERT: A 229 TYR cc_start: 0.9323 (t80) cc_final: 0.9061 (t80) REVERT: B 49 LEU cc_start: 0.9415 (mt) cc_final: 0.9184 (mt) REVERT: B 50 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8730 (mm-30) REVERT: B 111 LEU cc_start: 0.8806 (mt) cc_final: 0.8517 (mp) REVERT: B 214 ASP cc_start: 0.7123 (t0) cc_final: 0.6539 (t0) REVERT: B 217 ASN cc_start: 0.9298 (m-40) cc_final: 0.9034 (m-40) REVERT: B 227 TRP cc_start: 0.8786 (m100) cc_final: 0.8449 (m-10) REVERT: C 50 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8728 (mm-30) REVERT: C 111 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8561 (mp) REVERT: C 124 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8114 (mmmt) REVERT: C 170 GLU cc_start: 0.9192 (tt0) cc_final: 0.8942 (tt0) REVERT: C 227 TRP cc_start: 0.8779 (m100) cc_final: 0.8447 (m-10) REVERT: C 235 ILE cc_start: 0.9139 (mt) cc_final: 0.8890 (mt) REVERT: D 49 LEU cc_start: 0.9513 (mt) cc_final: 0.9233 (mt) REVERT: D 50 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8579 (mm-30) REVERT: D 60 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8964 (ttm) REVERT: D 65 MET cc_start: 0.8514 (ttt) cc_final: 0.8266 (tpt) REVERT: D 111 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8640 (mp) REVERT: D 124 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8474 (mmmt) REVERT: D 146 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7907 (mp0) REVERT: D 149 ASP cc_start: 0.8047 (t70) cc_final: 0.7813 (t0) REVERT: D 155 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8795 (mp) REVERT: D 174 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8705 (mmt90) REVERT: D 242 PHE cc_start: 0.8461 (t80) cc_final: 0.7751 (m-80) outliers start: 37 outliers final: 20 residues processed: 239 average time/residue: 0.0686 time to fit residues: 22.5573 Evaluate side-chains 221 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A 143 HIS A 215 HIS C 196 GLN C 215 HIS D 196 GLN D 215 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.118729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088826 restraints weight = 16502.801| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.59 r_work: 0.3109 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8216 Z= 0.128 Angle : 0.539 8.582 11068 Z= 0.280 Chirality : 0.036 0.148 1220 Planarity : 0.003 0.030 1288 Dihedral : 12.411 76.429 1316 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.99 % Allowed : 19.90 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.40 (0.27), residues: 932 helix: 3.58 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.80 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 174 TYR 0.009 0.000 TYR A 240 PHE 0.030 0.001 PHE A 13 TRP 0.009 0.001 TRP D 227 HIS 0.008 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8216) covalent geometry : angle 0.53868 / 0.28 (11068) hydrogen bonds : bond 0.04596 / 3.24 ( 657) hydrogen bonds : angle 3.29774 / 2.51 ( 1971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9516 (mt) cc_final: 0.9284 (mt) REVERT: A 50 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8751 (mm-30) REVERT: A 111 LEU cc_start: 0.8794 (mp) cc_final: 0.8582 (mp) REVERT: A 129 ASN cc_start: 0.9231 (t0) cc_final: 0.8933 (t0) REVERT: A 147 MET cc_start: 0.8660 (ptp) cc_final: 0.8326 (ptt) REVERT: A 216 GLU cc_start: 0.8168 (pm20) cc_final: 0.7828 (pm20) REVERT: A 227 TRP cc_start: 0.8793 (m100) cc_final: 0.8506 (m-10) REVERT: B 49 LEU cc_start: 0.9435 (mt) cc_final: 0.9207 (mt) REVERT: B 50 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8803 (mm-30) REVERT: B 60 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8833 (ttm) REVERT: B 111 LEU cc_start: 0.8799 (mt) cc_final: 0.8483 (mp) REVERT: B 124 LYS cc_start: 0.8341 (mmmt) cc_final: 0.8019 (mttm) REVERT: B 214 ASP cc_start: 0.6996 (t0) cc_final: 0.6606 (t0) REVERT: B 221 LEU cc_start: 0.9528 (mt) cc_final: 0.9306 (mp) REVERT: B 227 TRP cc_start: 0.8763 (m100) cc_final: 0.8437 (m-10) REVERT: B 229 TYR cc_start: 0.9277 (t80) cc_final: 0.9056 (t80) REVERT: C 50 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8725 (mm-30) REVERT: C 111 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8531 (mp) REVERT: C 124 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8507 (mmmt) REVERT: C 214 ASP cc_start: 0.6862 (t0) cc_final: 0.6624 (t0) REVERT: C 227 TRP cc_start: 0.8775 (m100) cc_final: 0.8466 (m-10) REVERT: C 235 ILE cc_start: 0.9124 (mt) cc_final: 0.8861 (mt) REVERT: D 49 LEU cc_start: 0.9522 (mt) cc_final: 0.9255 (mt) REVERT: D 50 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8631 (mm-30) REVERT: D 96 PHE cc_start: 0.9079 (t80) cc_final: 0.8814 (t80) REVERT: D 111 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8604 (mp) REVERT: D 124 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8427 (mmmt) REVERT: D 149 ASP cc_start: 0.8016 (t70) cc_final: 0.7773 (t0) REVERT: D 155 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8802 (mp) REVERT: D 214 ASP cc_start: 0.6894 (t0) cc_final: 0.6690 (t0) REVERT: D 220 PHE cc_start: 0.8981 (t80) cc_final: 0.8615 (t80) REVERT: D 242 PHE cc_start: 0.8396 (t80) cc_final: 0.7683 (m-80) outliers start: 47 outliers final: 26 residues processed: 232 average time/residue: 0.0675 time to fit residues: 21.5286 Evaluate side-chains 224 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS C 215 HIS D 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.086184 restraints weight = 16791.523| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.63 r_work: 0.3030 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8216 Z= 0.134 Angle : 0.544 6.944 11068 Z= 0.284 Chirality : 0.036 0.128 1220 Planarity : 0.003 0.030 1288 Dihedral : 12.175 76.660 1316 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.48 % Allowed : 20.28 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.27 (0.27), residues: 932 helix: 3.48 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.80 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 174 TYR 0.007 0.001 TYR A 240 PHE 0.031 0.001 PHE D 13 TRP 0.010 0.001 TRP D 227 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8216) covalent geometry : angle 0.54417 / 0.28 (11068) hydrogen bonds : bond 0.04798 / 3.39 ( 657) hydrogen bonds : angle 3.38683 / 2.57 ( 1971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9529 (mt) cc_final: 0.9329 (mt) REVERT: A 50 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8829 (mm-30) REVERT: A 96 PHE cc_start: 0.9070 (t80) cc_final: 0.8820 (t80) REVERT: A 111 LEU cc_start: 0.8775 (mp) cc_final: 0.8568 (mp) REVERT: A 124 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8132 (mtpp) REVERT: A 147 MET cc_start: 0.8680 (ptp) cc_final: 0.8027 (ptt) REVERT: A 213 MET cc_start: 0.6910 (mmm) cc_final: 0.5917 (mmm) REVERT: A 229 TYR cc_start: 0.9285 (t80) cc_final: 0.8984 (t80) REVERT: B 50 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8877 (mm-30) REVERT: B 111 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 124 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8042 (mttm) REVERT: B 214 ASP cc_start: 0.7087 (t0) cc_final: 0.6584 (t0) REVERT: B 227 TRP cc_start: 0.8794 (m100) cc_final: 0.8460 (m-10) REVERT: C 49 LEU cc_start: 0.9456 (mt) cc_final: 0.9232 (mt) REVERT: C 50 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8811 (mm-30) REVERT: C 96 PHE cc_start: 0.9031 (t80) cc_final: 0.8788 (t80) REVERT: C 111 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8564 (mp) REVERT: C 124 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8470 (mmmt) REVERT: C 170 GLU cc_start: 0.9284 (tt0) cc_final: 0.9074 (tt0) REVERT: C 214 ASP cc_start: 0.6992 (t0) cc_final: 0.6517 (t0) REVERT: C 227 TRP cc_start: 0.8792 (m100) cc_final: 0.8461 (m-10) REVERT: C 235 ILE cc_start: 0.9155 (mt) cc_final: 0.8898 (mt) REVERT: D 50 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8710 (mm-30) REVERT: D 96 PHE cc_start: 0.9062 (t80) cc_final: 0.8770 (t80) REVERT: D 111 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8561 (mp) REVERT: D 124 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8441 (mmmt) REVERT: D 129 ASN cc_start: 0.9331 (t0) cc_final: 0.9021 (t0) REVERT: D 149 ASP cc_start: 0.8035 (t70) cc_final: 0.7777 (t0) REVERT: D 155 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8830 (mp) REVERT: D 174 ARG cc_start: 0.9013 (mmm-85) cc_final: 0.8586 (mmt90) REVERT: D 214 ASP cc_start: 0.6894 (t0) cc_final: 0.6523 (t0) REVERT: D 229 TYR cc_start: 0.9257 (t80) cc_final: 0.9048 (t80) REVERT: D 242 PHE cc_start: 0.8390 (t80) cc_final: 0.7665 (m-80) outliers start: 43 outliers final: 30 residues processed: 229 average time/residue: 0.0648 time to fit residues: 20.3627 Evaluate side-chains 230 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 3 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 28 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS D 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089972 restraints weight = 16594.947| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.58 r_work: 0.3069 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8216 Z= 0.126 Angle : 0.548 6.969 11068 Z= 0.284 Chirality : 0.037 0.188 1220 Planarity : 0.003 0.030 1288 Dihedral : 11.822 75.528 1316 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.36 % Allowed : 20.28 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.27), residues: 932 helix: 3.43 (0.17), residues: 776 sheet: None (None), residues: 0 loop : -0.84 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 174 TYR 0.005 0.000 TYR C 229 PHE 0.029 0.001 PHE B 13 TRP 0.011 0.001 TRP D 227 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 8216) covalent geometry : angle 0.54809 / 0.28 (11068) hydrogen bonds : bond 0.04524 / 3.20 ( 657) hydrogen bonds : angle 3.39599 / 2.58 ( 1971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8527 (t80) cc_final: 0.8182 (t80) REVERT: A 50 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8867 (mm-30) REVERT: A 96 PHE cc_start: 0.9103 (t80) cc_final: 0.8859 (t80) REVERT: A 111 LEU cc_start: 0.8780 (mp) cc_final: 0.8562 (mp) REVERT: A 147 MET cc_start: 0.8671 (ptp) cc_final: 0.8186 (ptt) REVERT: A 213 MET cc_start: 0.6819 (mmm) cc_final: 0.6117 (mmm) REVERT: A 227 TRP cc_start: 0.8756 (m100) cc_final: 0.8478 (m-10) REVERT: A 229 TYR cc_start: 0.9278 (t80) cc_final: 0.9068 (t80) REVERT: B 49 LEU cc_start: 0.9475 (mt) cc_final: 0.9241 (mp) REVERT: B 50 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8946 (mm-30) REVERT: B 111 LEU cc_start: 0.8735 (mt) cc_final: 0.8442 (mp) REVERT: B 124 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8071 (mttm) REVERT: B 214 ASP cc_start: 0.7166 (t0) cc_final: 0.6642 (t0) REVERT: B 227 TRP cc_start: 0.8772 (m100) cc_final: 0.8443 (m-10) REVERT: C 49 LEU cc_start: 0.9465 (mt) cc_final: 0.9260 (mt) REVERT: C 50 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8798 (mm-30) REVERT: C 96 PHE cc_start: 0.9038 (t80) cc_final: 0.8764 (t80) REVERT: C 111 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8503 (mp) REVERT: C 124 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8398 (mmmt) REVERT: C 213 MET cc_start: 0.6980 (mmm) cc_final: 0.4999 (mmm) REVERT: C 214 ASP cc_start: 0.6997 (t0) cc_final: 0.6525 (t0) REVERT: C 227 TRP cc_start: 0.8757 (m100) cc_final: 0.8454 (m-10) REVERT: C 235 ILE cc_start: 0.9126 (mt) cc_final: 0.8864 (mt) REVERT: D 50 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8830 (mm-30) REVERT: D 111 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8515 (mp) REVERT: D 124 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8348 (mmmt) REVERT: D 129 ASN cc_start: 0.9310 (t0) cc_final: 0.9018 (t0) REVERT: D 149 ASP cc_start: 0.8001 (t70) cc_final: 0.7759 (t0) REVERT: D 155 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8795 (mp) REVERT: D 214 ASP cc_start: 0.6833 (t0) cc_final: 0.6405 (t0) REVERT: D 242 PHE cc_start: 0.8363 (t80) cc_final: 0.7643 (m-80) outliers start: 42 outliers final: 30 residues processed: 229 average time/residue: 0.0670 time to fit residues: 21.1074 Evaluate side-chains 228 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 3 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 82 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS C 143 HIS D 34 GLN D 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.119075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088869 restraints weight = 16628.517| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.66 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8216 Z= 0.131 Angle : 0.578 9.049 11068 Z= 0.298 Chirality : 0.036 0.150 1220 Planarity : 0.003 0.030 1288 Dihedral : 11.691 74.455 1316 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.85 % Allowed : 21.68 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.13 (0.27), residues: 932 helix: 3.36 (0.17), residues: 776 sheet: None (None), residues: 0 loop : -0.92 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 174 TYR 0.007 0.000 TYR C 229 PHE 0.032 0.001 PHE C 96 TRP 0.014 0.001 TRP D 227 HIS 0.006 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8216) covalent geometry : angle 0.57833 / 0.30 (11068) hydrogen bonds : bond 0.04596 / 3.24 ( 657) hydrogen bonds : angle 3.46524 / 2.63 ( 1971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 PHE cc_start: 0.8383 (t80) cc_final: 0.8127 (t80) REVERT: A 50 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8835 (mm-30) REVERT: A 96 PHE cc_start: 0.9181 (t80) cc_final: 0.8745 (t80) REVERT: A 111 LEU cc_start: 0.8826 (mp) cc_final: 0.8619 (mp) REVERT: A 147 MET cc_start: 0.8450 (ptp) cc_final: 0.8120 (ptt) REVERT: A 213 MET cc_start: 0.6781 (mmm) cc_final: 0.6378 (mmm) REVERT: A 214 ASP cc_start: 0.7351 (t0) cc_final: 0.7042 (t0) REVERT: A 217 ASN cc_start: 0.8874 (m-40) cc_final: 0.8461 (m-40) REVERT: B 124 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7936 (mttm) REVERT: B 214 ASP cc_start: 0.7633 (t0) cc_final: 0.7087 (t0) REVERT: B 215 HIS cc_start: 0.8484 (m-70) cc_final: 0.8218 (m-70) REVERT: B 221 LEU cc_start: 0.9513 (mp) cc_final: 0.9269 (mp) REVERT: B 227 TRP cc_start: 0.8595 (m100) cc_final: 0.8292 (m-10) REVERT: C 50 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8759 (mm-30) REVERT: C 96 PHE cc_start: 0.9199 (t80) cc_final: 0.8706 (t80) REVERT: C 111 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8536 (mp) REVERT: C 214 ASP cc_start: 0.7335 (t0) cc_final: 0.6903 (t0) REVERT: C 227 TRP cc_start: 0.8590 (m100) cc_final: 0.8334 (m-10) REVERT: C 235 ILE cc_start: 0.9130 (mt) cc_final: 0.8888 (mt) REVERT: D 50 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8762 (mm-30) REVERT: D 96 PHE cc_start: 0.9177 (t80) cc_final: 0.8748 (t80) REVERT: D 111 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8606 (mp) REVERT: D 149 ASP cc_start: 0.7907 (t70) cc_final: 0.7646 (t0) REVERT: D 214 ASP cc_start: 0.6874 (t0) cc_final: 0.6422 (t0) REVERT: D 221 LEU cc_start: 0.9508 (mt) cc_final: 0.9256 (mp) REVERT: D 242 PHE cc_start: 0.8328 (t80) cc_final: 0.7671 (m-80) outliers start: 38 outliers final: 32 residues processed: 232 average time/residue: 0.0651 time to fit residues: 20.8899 Evaluate side-chains 235 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 3 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN A 215 HIS ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS D 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.118945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087700 restraints weight = 16885.160| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.68 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8216 Z= 0.139 Angle : 0.604 9.310 11068 Z= 0.310 Chirality : 0.037 0.151 1220 Planarity : 0.003 0.031 1288 Dihedral : 11.717 73.721 1316 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.59 % Allowed : 22.70 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.27), residues: 932 helix: 3.30 (0.17), residues: 776 sheet: None (None), residues: 0 loop : -0.90 (0.55), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 174 TYR 0.008 0.001 TYR B 229 PHE 0.042 0.001 PHE D 13 TRP 0.015 0.001 TRP D 227 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8216) covalent geometry : angle 0.60415 / 0.31 (11068) hydrogen bonds : bond 0.04792 / 3.39 ( 657) hydrogen bonds : angle 3.59196 / 2.72 ( 1971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8870 (mm-30) REVERT: A 96 PHE cc_start: 0.9177 (t80) cc_final: 0.8744 (t80) REVERT: A 111 LEU cc_start: 0.8791 (mp) cc_final: 0.8585 (mp) REVERT: A 147 MET cc_start: 0.8486 (ptp) cc_final: 0.8067 (ptt) REVERT: A 213 MET cc_start: 0.6979 (mmm) cc_final: 0.6439 (mmm) REVERT: A 214 ASP cc_start: 0.7299 (t0) cc_final: 0.6535 (t0) REVERT: A 217 ASN cc_start: 0.9208 (m-40) cc_final: 0.8880 (m-40) REVERT: B 111 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8463 (mp) REVERT: B 124 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7953 (mttm) REVERT: B 214 ASP cc_start: 0.7646 (t0) cc_final: 0.7089 (t0) REVERT: B 215 HIS cc_start: 0.8609 (m-70) cc_final: 0.8348 (m-70) REVERT: B 221 LEU cc_start: 0.9507 (mp) cc_final: 0.9296 (mp) REVERT: B 227 TRP cc_start: 0.8586 (m100) cc_final: 0.8283 (m-10) REVERT: C 4 PHE cc_start: 0.8641 (t80) cc_final: 0.8428 (t80) REVERT: C 50 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8826 (mm-30) REVERT: C 96 PHE cc_start: 0.9205 (t80) cc_final: 0.8786 (t80) REVERT: C 111 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8492 (mp) REVERT: C 214 ASP cc_start: 0.7394 (t0) cc_final: 0.6841 (t0) REVERT: C 227 TRP cc_start: 0.8584 (m100) cc_final: 0.8310 (m-10) REVERT: C 235 ILE cc_start: 0.9088 (mt) cc_final: 0.8835 (mt) REVERT: D 50 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8801 (mm-30) REVERT: D 111 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8604 (mp) REVERT: D 124 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7984 (mttm) REVERT: D 149 ASP cc_start: 0.7896 (t70) cc_final: 0.7637 (t0) REVERT: D 221 LEU cc_start: 0.9493 (mt) cc_final: 0.9236 (mp) REVERT: D 235 ILE cc_start: 0.9103 (mt) cc_final: 0.8884 (mt) REVERT: D 242 PHE cc_start: 0.8322 (t80) cc_final: 0.7650 (m-80) outliers start: 36 outliers final: 31 residues processed: 230 average time/residue: 0.0755 time to fit residues: 23.8351 Evaluate side-chains 236 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 3 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 0.2980 chunk 90 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 HIS ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.116448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084715 restraints weight = 16848.357| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.67 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8216 Z= 0.167 Angle : 0.670 9.928 11068 Z= 0.343 Chirality : 0.038 0.203 1220 Planarity : 0.003 0.031 1288 Dihedral : 12.038 74.002 1316 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.21 % Allowed : 23.60 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.93 (0.27), residues: 932 helix: 3.24 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.87 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 174 TYR 0.008 0.001 TYR D 229 PHE 0.042 0.002 PHE D 13 TRP 0.022 0.001 TRP D 227 HIS 0.011 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 8216) covalent geometry : angle 0.66965 / 0.34 (11068) hydrogen bonds : bond 0.05587 / 3.96 ( 657) hydrogen bonds : angle 3.79724 / 2.89 ( 1971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8893 (mm-30) REVERT: A 96 PHE cc_start: 0.9218 (t80) cc_final: 0.8785 (t80) REVERT: A 111 LEU cc_start: 0.8850 (mp) cc_final: 0.8617 (mp) REVERT: A 124 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8134 (mtpp) REVERT: A 129 ASN cc_start: 0.9159 (t0) cc_final: 0.8926 (t0) REVERT: A 147 MET cc_start: 0.8505 (ptp) cc_final: 0.7881 (ptt) REVERT: A 213 MET cc_start: 0.7114 (mmm) cc_final: 0.6469 (mmm) REVERT: A 214 ASP cc_start: 0.7207 (t0) cc_final: 0.6512 (t0) REVERT: A 217 ASN cc_start: 0.9178 (m-40) cc_final: 0.8908 (m-40) REVERT: B 111 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8577 (mp) REVERT: B 214 ASP cc_start: 0.7599 (t0) cc_final: 0.7154 (t0) REVERT: B 221 LEU cc_start: 0.9519 (mp) cc_final: 0.9285 (mp) REVERT: B 227 TRP cc_start: 0.8616 (m100) cc_final: 0.8367 (m-10) REVERT: B 229 TYR cc_start: 0.9218 (t80) cc_final: 0.9003 (t80) REVERT: C 96 PHE cc_start: 0.9174 (t80) cc_final: 0.8755 (t80) REVERT: C 111 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8630 (mp) REVERT: C 214 ASP cc_start: 0.7260 (t0) cc_final: 0.6877 (t0) REVERT: C 227 TRP cc_start: 0.8656 (m100) cc_final: 0.8311 (m-10) REVERT: C 229 TYR cc_start: 0.9306 (t80) cc_final: 0.9017 (t80) REVERT: C 235 ILE cc_start: 0.9121 (mt) cc_final: 0.8838 (mt) REVERT: D 50 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8813 (mm-30) REVERT: D 96 PHE cc_start: 0.9223 (t80) cc_final: 0.8652 (t80) REVERT: D 111 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8679 (mp) REVERT: D 146 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8098 (mp0) REVERT: D 149 ASP cc_start: 0.7964 (t70) cc_final: 0.7711 (t0) REVERT: D 216 GLU cc_start: 0.8108 (pm20) cc_final: 0.7832 (pm20) REVERT: D 217 ASN cc_start: 0.9091 (m-40) cc_final: 0.8449 (m-40) REVERT: D 221 LEU cc_start: 0.9532 (mt) cc_final: 0.9288 (mp) REVERT: D 242 PHE cc_start: 0.8273 (t80) cc_final: 0.7626 (m-80) outliers start: 33 outliers final: 27 residues processed: 225 average time/residue: 0.0744 time to fit residues: 23.0231 Evaluate side-chains 233 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 3 ASN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.079403 restraints weight = 16948.024| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.53 r_work: 0.2905 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 8216 Z= 0.274 Angle : 0.776 11.957 11068 Z= 0.404 Chirality : 0.041 0.179 1220 Planarity : 0.004 0.030 1288 Dihedral : 13.215 77.868 1316 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.95 % Allowed : 24.74 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.27), residues: 932 helix: 2.91 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.82 (0.53), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 174 TYR 0.012 0.001 TYR C 240 PHE 0.028 0.002 PHE A 13 TRP 0.032 0.002 TRP D 227 HIS 0.011 0.001 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.27 ( 8216) covalent geometry : angle 0.77624 / 0.40 (11068) hydrogen bonds : bond 0.07401 / 5.15 ( 657) hydrogen bonds : angle 4.32172 / 3.29 ( 1971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.94 seconds wall clock time: 25 minutes 41.26 seconds (1541.26 seconds total)